date:20171101

Re: [gmx-users] Lost particles while sorting

2017-11-01 Thread Alex

Will upload to dropbox later (strict 'no external cloud' institutional
policy). I don't know if the tpr is completely self-contained, so please
let me know if you need the ff folder as well.

Thank you,

Alex

On Wed, Nov 1, 2017 at 4:42 PM, Mark Abraham 
wrote:

> Hi,
>
> We have had several reports of "lost particles while sorting" but we would
> like a .tpr on an issue on redmine.gromacs.org to be able to investigate,
> please!
>
> Mark
>
> On Wed, Nov 1, 2017 at 10:19 PM Alex  wrote:
>
> > Hi all,
> >
> > I am using walls in the cowboy mode, GMX v. 2016.3, system is a porous
> > membrane (periodic in XY) with water and ions -- everything works fine
> with
> > pbc=xyz and no walls. With walls, mdrun throws "Software inconsistency
> > error: Lost particles while sorting."
> >
> > mdp exerpt below:
> >
> > pbc = xy
> > nwall   = 2
> > wall-type   = 12-6
> > wall-r-linpot   = 0.0
> > wall_atomtype   = opls_996 opls_996
> > wall-ewald-zfac = 3
> > periodic_molecules  = yes
> > ns_type =  grid
> > rlist   =  1.0
> > coulombtype =  pme
> > ewald-geometry  =  3dc
> > fourierspacing  =  0.135
> > rcoulomb=  1.0
> > rvdw=  1.0
> > vdwtype =  cut-off
> > cutoff-scheme   = Verlet
> >
> > This uses a custom type "opls_996" properly defined in ffnonbonded of the
> > FF (custom OPLSAA). Any suggestions? I can provide more info, if needed.
> >
> > Thank you,
> >
> > Alex
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Lost particles while sorting

2017-11-01 Thread Mark Abraham

Hi,

We have had several reports of "lost particles while sorting" but we would
like a .tpr on an issue on redmine.gromacs.org to be able to investigate,
please!

Mark

On Wed, Nov 1, 2017 at 10:19 PM Alex  wrote:

> Hi all,
>
> I am using walls in the cowboy mode, GMX v. 2016.3, system is a porous
> membrane (periodic in XY) with water and ions -- everything works fine with
> pbc=xyz and no walls. With walls, mdrun throws "Software inconsistency
> error: Lost particles while sorting."
>
> mdp exerpt below:
>
> pbc = xy
> nwall   = 2
> wall-type   = 12-6
> wall-r-linpot   = 0.0
> wall_atomtype   = opls_996 opls_996
> wall-ewald-zfac = 3
> periodic_molecules  = yes
> ns_type =  grid
> rlist   =  1.0
> coulombtype =  pme
> ewald-geometry  =  3dc
> fourierspacing  =  0.135
> rcoulomb=  1.0
> rvdw=  1.0
> vdwtype =  cut-off
> cutoff-scheme   = Verlet
>
> This uses a custom type "opls_996" properly defined in ffnonbonded of the
> FF (custom OPLSAA). Any suggestions? I can provide more info, if needed.
>
> Thank you,
>
> Alex
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Lost particles while sorting

2017-11-01 Thread Alex

Hi all,

I am using walls in the cowboy mode, GMX v. 2016.3, system is a porous
membrane (periodic in XY) with water and ions -- everything works fine with
pbc=xyz and no walls. With walls, mdrun throws "Software inconsistency
error: Lost particles while sorting."

mdp exerpt below:

pbc = xy
nwall   = 2
wall-type   = 12-6
wall-r-linpot   = 0.0
wall_atomtype   = opls_996 opls_996
wall-ewald-zfac = 3
periodic_molecules  = yes
ns_type =  grid
rlist   =  1.0
coulombtype =  pme
ewald-geometry  =  3dc
fourierspacing  =  0.135
rcoulomb=  1.0
rvdw=  1.0
vdwtype =  cut-off
cutoff-scheme   = Verlet

This uses a custom type "opls_996" properly defined in ffnonbonded of the
FF (custom OPLSAA). Any suggestions? I can provide more info, if needed.

Thank you,

Alex
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Problem using gmx wham

2017-11-01 Thread Jefferies D . F .

Hi,

I am attempting to use gmx wham to compute a potential of mean force. I have 
used the command line:

gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ

where tpr-files.dat and pullf-files.dat contain a list of the .tpr and 
pullf.xvg files from each umbrella sampling window, respectively.

It seems that gmx wham is having trouble reading the .tpr and .xvg files, as I 
get this error message:

---

Program gmx wham, VERSION 5.1.4

Source code file: 
/local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp,
 line: 1800


Fatal error:

Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.


For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

---


I have computed potential of mean force profiles before (using this Mac), but I 
haven't encountered this problem. Could someone help me with this problem?


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Problem on continuing MD

2017-11-01 Thread YanhuaOuyang

Dear Mark,


Thank you so much. I have read the linked website you told and know why such 
problem happens.


Best regards,
Ouyang 








At 2017-11-01 17:39:17, "Mark Abraham"  wrote:
>Hi,
>
>See http://www.gromacs.org/Documentation/Terminology/Reproducibility. You
>have non-reproducible load balancing. However this is not a problem unless
>your experimental design hinges upon being able to reproduce an exact
>trajectory (in which case you will have a tough time getting performance).
>You would get a different trajectory if you rotated your initial system by
>90 degrees too. Which one is "right?"
>
>Mark
>
>On Wed, Nov 1, 2017 at 10:20 AM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Dear gromacs user,
>>
>>
>>Today, I continue the MD twice in two directories from the same
>> point of the MD trajectory, for example 100ns, using the same CPU, same
>> checkpoint file, same serve node. To my surprise, the energy informations
>> are different between the two continued log ouput files, which are shown
>> below.
>>
>>
>> continue_md_01.log:
>>
>> Started mdrun on rank 0 Wed Nov  1 23:17:08 2017
>>
>>Step   Time Lambda
>>
>>5000   10.00.0
>>
>>Energies (kJ/mol)
>>
>>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>>
>> 4.67507e+021.47390e+031.44019e+036.93280e+018.29478e+01
>>
>>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
>>
>> 4.17297e+029.82076e+031.12930e+05   -8.68735e+03   -1.15522e+06
>>
>>Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.
>>
>> 5.88613e+03   -1.03132e+061.63796e+05   -8.67527e+05   -1.90771e+05
>>
>> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>>
>> 2.82366e+02   -2.04258e+02   -7.74514e+022.31539e-06
>>
>> DD  step 5019 load imb.: force 29.5%  pme mesh/force 0.964
>>
>> At step 5020 the performance loss due to force load imbalance is 11.1 %
>>
>>Step   Time Lambda
>>
>>50001000   12.00.0
>>
>>Energies (kJ/mol)
>>
>>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>>
>> 4.65447e+021.50124e+031.50444e+037.92082e+011.64421e+01
>>
>>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
>>
>> 4.18616e+029.80230e+031.11198e+05   -8.68735e+03   -1.15433e+06
>>
>>Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.
>>
>> 5.95908e+03   -1.03208e+061.64017e+05   -8.68059e+05   -1.90761e+05
>>
>> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>>
>> 2.82747e+02   -2.04258e+02   -9.31332e+023.06123e-06
>>
>> DD  step 50001999  vol min/aver 0.880  load imb.: force 10.0%  pme
>> mesh/force 1.059
>>
>> ...
>>
>>
>>
>>
>> continue_md_02.log:
>>
>> Started mdrun on rank 0 Wed Nov  1 23:39:51 2017
>>
>>Step   Time Lambda
>>
>>5000   10.00.0
>>
>>Energies (kJ/mol)
>>
>>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>>
>> 4.67507e+021.47390e+031.44019e+036.93280e+018.29478e+01
>>
>>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
>>
>> 4.17297e+029.82076e+031.12930e+05   -8.68735e+03   -1.15522e+06
>>
>>Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.
>>
>> 5.88613e+03   -1.03132e+061.63796e+05   -8.67527e+05   -1.90771e+05
>>
>> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>>
>> 2.82366e+02   -2.04258e+02   -7.74505e+022.31539e-06
>>
>> DD  step 5019 load imb.: force 18.3%  pme mesh/force 0.950
>>
>> At step 5020 the performance loss due to force load imbalance is 6.9 %
>>
>>Step   Time Lambda
>>
>>50001000   12.00.0
>>
>>Energies (kJ/mol)
>>
>>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>>
>> 4.51321e+021.43914e+031.56368e+039.15439e+011.64274e+01
>>
>>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
>>
>> 4.07426e+029.84156e+031.12168e+05   -8.68735e+03   -1.15440e+06
>>
>>Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.
>>
>> 5.88309e+03   -1.03123e+061.62769e+05   -8.68456e+05   -1.90745e+05
>>
>> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>>
>> 2.80597e+02   -2.04258e+02   -8.80279e+022.64599e-06
>>
>> DD  step 50001999  vol min/aver 0.905  load imb.: force 32.7%  pme
>> mesh/force 1.034
>>
>>...
>>
>>
>>
>>
>> It is obviously shown that the energy informations varied from 12ps
>> (the md is continued from 100ns). Generally speaking, the two continued MD
>> should be same each other since the conditions are

Re: [gmx-users] Problem on continuing MD

2017-11-01 Thread Mark Abraham

Hi,

See http://www.gromacs.org/Documentation/Terminology/Reproducibility. You
have non-reproducible load balancing. However this is not a problem unless
your experimental design hinges upon being able to reproduce an exact
trajectory (in which case you will have a tough time getting performance).
You would get a different trajectory if you rotated your initial system by
90 degrees too. Which one is "right?"

Mark

On Wed, Nov 1, 2017 at 10:20 AM YanhuaOuyang <15901283...@163.com> wrote:

> Dear gromacs user,
>
>
>Today, I continue the MD twice in two directories from the same
> point of the MD trajectory, for example 100ns, using the same CPU, same
> checkpoint file, same serve node. To my surprise, the energy informations
> are different between the two continued log ouput files, which are shown
> below.
>
>
> continue_md_01.log:
>
> Started mdrun on rank 0 Wed Nov  1 23:17:08 2017
>
>Step   Time Lambda
>
>5000   10.00.0
>
>Energies (kJ/mol)
>
>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>
> 4.67507e+021.47390e+031.44019e+036.93280e+018.29478e+01
>
>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
>
> 4.17297e+029.82076e+031.12930e+05   -8.68735e+03   -1.15522e+06
>
>Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.
>
> 5.88613e+03   -1.03132e+061.63796e+05   -8.67527e+05   -1.90771e+05
>
> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>
> 2.82366e+02   -2.04258e+02   -7.74514e+022.31539e-06
>
> DD  step 5019 load imb.: force 29.5%  pme mesh/force 0.964
>
> At step 5020 the performance loss due to force load imbalance is 11.1 %
>
>Step   Time Lambda
>
>50001000   12.00.0
>
>Energies (kJ/mol)
>
>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>
> 4.65447e+021.50124e+031.50444e+037.92082e+011.64421e+01
>
>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
>
> 4.18616e+029.80230e+031.11198e+05   -8.68735e+03   -1.15433e+06
>
>Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.
>
> 5.95908e+03   -1.03208e+061.64017e+05   -8.68059e+05   -1.90761e+05
>
> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>
> 2.82747e+02   -2.04258e+02   -9.31332e+023.06123e-06
>
> DD  step 50001999  vol min/aver 0.880  load imb.: force 10.0%  pme
> mesh/force 1.059
>
> ...
>
>
>
>
> continue_md_02.log:
>
> Started mdrun on rank 0 Wed Nov  1 23:39:51 2017
>
>Step   Time Lambda
>
>5000   10.00.0
>
>Energies (kJ/mol)
>
>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>
> 4.67507e+021.47390e+031.44019e+036.93280e+018.29478e+01
>
>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
>
> 4.17297e+029.82076e+031.12930e+05   -8.68735e+03   -1.15522e+06
>
>Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.
>
> 5.88613e+03   -1.03132e+061.63796e+05   -8.67527e+05   -1.90771e+05
>
> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>
> 2.82366e+02   -2.04258e+02   -7.74505e+022.31539e-06
>
> DD  step 5019 load imb.: force 18.3%  pme mesh/force 0.950
>
> At step 5020 the performance loss due to force load imbalance is 6.9 %
>
>Step   Time Lambda
>
>50001000   12.00.0
>
>Energies (kJ/mol)
>
>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
>
> 4.51321e+021.43914e+031.56368e+039.15439e+011.64274e+01
>
>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
>
> 4.07426e+029.84156e+031.12168e+05   -8.68735e+03   -1.15440e+06
>
>Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.
>
> 5.88309e+03   -1.03123e+061.62769e+05   -8.68456e+05   -1.90745e+05
>
> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
>
> 2.80597e+02   -2.04258e+02   -8.80279e+022.64599e-06
>
> DD  step 50001999  vol min/aver 0.905  load imb.: force 32.7%  pme
> mesh/force 1.034
>
>...
>
>
>
>
> It is obviously shown that the energy informations varied from 12ps
> (the md is continued from 100ns). Generally speaking, the two continued MD
> should be same each other since the conditions are same.
> Why are they different? Does it mean the MD can not be terminated or
> transfered from one server to another because they are changeable if we
> want to investigate the dynamic property?
> Do anyone knows the problems?
>
>
>
>
> Best regards,
> Ouyang.
>
>
>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
>

[gmx-users] Problem on continuing MD

2017-11-01 Thread YanhuaOuyang

Dear gromacs user,


   Today, I continue the MD twice in two directories from the same point of 
the MD trajectory, for example 100ns, using the same CPU, same checkpoint file, 
same serve node. To my surprise, the energy informations are different between 
the two continued log ouput files, which are shown below. 


continue_md_01.log:

Started mdrun on rank 0 Wed Nov  1 23:17:08 2017

   Step   Time Lambda

   5000   10.00.0

   Energies (kJ/mol)

   BondU-BProper Dih.  Improper Dih.  CMAP Dih.

4.67507e+021.47390e+031.44019e+036.93280e+018.29478e+01

  LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)

4.17297e+029.82076e+031.12930e+05   -8.68735e+03   -1.15522e+06

   Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.

5.88613e+03   -1.03132e+061.63796e+05   -8.67527e+05   -1.90771e+05

Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd

2.82366e+02   -2.04258e+02   -7.74514e+022.31539e-06

DD  step 5019 load imb.: force 29.5%  pme mesh/force 0.964

At step 5020 the performance loss due to force load imbalance is 11.1 %

   Step   Time Lambda

   50001000   12.00.0

   Energies (kJ/mol)

   BondU-BProper Dih.  Improper Dih.  CMAP Dih.

4.65447e+021.50124e+031.50444e+037.92082e+011.64421e+01

  LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)

4.18616e+029.80230e+031.11198e+05   -8.68735e+03   -1.15433e+06

   Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.

5.95908e+03   -1.03208e+061.64017e+05   -8.68059e+05   -1.90761e+05

Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd

2.82747e+02   -2.04258e+02   -9.31332e+023.06123e-06

DD  step 50001999  vol min/aver 0.880  load imb.: force 10.0%  pme mesh/force 
1.059

...




continue_md_02.log:

Started mdrun on rank 0 Wed Nov  1 23:39:51 2017

   Step   Time Lambda

   5000   10.00.0

   Energies (kJ/mol)

   BondU-BProper Dih.  Improper Dih.  CMAP Dih.

4.67507e+021.47390e+031.44019e+036.93280e+018.29478e+01

  LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)

4.17297e+029.82076e+031.12930e+05   -8.68735e+03   -1.15522e+06

   Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.

5.88613e+03   -1.03132e+061.63796e+05   -8.67527e+05   -1.90771e+05

Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd

2.82366e+02   -2.04258e+02   -7.74505e+022.31539e-06

DD  step 5019 load imb.: force 18.3%  pme mesh/force 0.950

At step 5020 the performance loss due to force load imbalance is 6.9 %

   Step   Time Lambda

   50001000   12.00.0

   Energies (kJ/mol)

   BondU-BProper Dih.  Improper Dih.  CMAP Dih.

4.51321e+021.43914e+031.56368e+039.15439e+011.64274e+01

  LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)

4.07426e+029.84156e+031.12168e+05   -8.68735e+03   -1.15440e+06

   Coul. recip.  PotentialKinetic En.   Total Energy  Conserved En.

5.88309e+03   -1.03123e+061.62769e+05   -8.68456e+05   -1.90745e+05

Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd

2.80597e+02   -2.04258e+02   -8.80279e+022.64599e-06

DD  step 50001999  vol min/aver 0.905  load imb.: force 32.7%  pme mesh/force 
1.034

   ...




It is obviously shown that the energy informations varied from 12ps (the md 
is continued from 100ns). Generally speaking, the two continued MD should be 
same each other since the conditions are same.
Why are they different? Does it mean the MD can not be terminated or transfered 
from one server to another because they are changeable if we want to 
investigate the dynamic property?
Do anyone knows the problems?




Best regards,
Ouyang.






-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Amino Acids

2017-11-01 Thread Mark Abraham

Hi,

Please try to keep to one email per question :-) Did you read the paper to
learn what termini they used?

Mark

On Wed, 1 Nov 2017 07:34 rose rahmani  wrote:

> Hi
>
> If  standalone amino acids are zwitterionic and inappropriate for AMBER and
> GROMACS ,what do you think about this article?!
>
> Interactions of aqueous amino acids and proteins with the (110) surface of
> ZnS in molecular dynamics simulations
> *Article* in The Journal of Chemical Physics 140(9):095101 · March 2014
> DOI: 10.1063/1.4866763 · Source:PubMed
> <
> https://www.researchgate.net/publication/deref/http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F24606380
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Amino Acids

2017-11-01 Thread rose rahmani

Hi

If  standalone amino acids are zwitterionic and inappropriate for AMBER and
GROMACS ,what do you think about this article?!

Interactions of aqueous amino acids and proteins with the (110) surface of
ZnS in molecular dynamics simulations
*Article* in The Journal of Chemical Physics 140(9):095101 · March 2014
DOI: 10.1063/1.4866763 · Source:PubMed



sorry for repeating again and again
With Regards
Rose
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Amino Acids

2017-11-01 Thread rose rahmani

Hi

If  standalone amino acids are zwitterionic and inappropriate for AMBER and
GROMACS ,what do you think about this article?!

Interactions of aqueous amino acids and proteins with the (110) surface of
ZnS in molecular dynamics simulations
*Article* in The Journal of Chemical Physics 140(9):095101 · March 2014
DOI: 10.1063/1.4866763 · Source:PubMed

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Amino Acids

2017-11-01 Thread rose rahmani

Hi

If  standalone amino acids are zwitterionic and inappropriate for AMBER and
GROMACS ,what do you think about this article?!

Interactions of aqueous amino acids and proteins with the (110) surface of
ZnS in molecular dynamics simulations
*Article* in The Journal of Chemical Physics 140(9):095101 · March 2014
DOI: 10.1063/1.4866763 · Source:PubMed


sorry for asking again and again With Regards
Rose
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Fwd: Amino acids

2017-11-01 Thread rose rahmani

-- Forwarded message --
From: Rose 
Date: Wed, Nov 1, 2017 at 1:06 AM
Subject: Amino acids
To: Gromacs 

Hi

If  standalone amino acids are zwitterionic and inappropriate for AMBER and
GROMACS ,what do you think about this article?!

Interactions of aqueous amino acids and proteins with the (110) surface of
ZnS in molecular dynamics simulations
*Article* in The Journal of Chemical Physics 140(9):095101 · March 2014
DOI: 10.1063/1.4866763 · Source:PubMed

Sorry for asking again and again

With regards
Sent from my iPhone
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] force field for selinomethionine?

2017-11-01 Thread Seera Suryanarayana

Dear gromacs users,

I have to do simulations for a peptide which has the selinomethionine. But
regular force fields from gromacs has no information for this residue.
kindly give me information if is there any force field for
selinometheoinine.

Thanks in advance
Surya
Graduate student
India.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Problem in calculating static dielectric constant of Lysozymes

2017-11-01 Thread David van der Spoel


On 31/10/17 20:56, Suman Das wrote:

Dear Gromacs Users,

I am trying to calculate static dielectric constant of Lysozymes using
gromacs version 4.6.7. I tried to follow the protocol used earlier by van
Gunsteren (J. Phys. Chem. 1993, 97, 2009-2014).  I used PME for the
electrostatic interaction. First, I converted the trajectory of protein by
using the command 'trjconv -f traj.xtc -o protein.xtc -pbc whole -e
1000.0". Then I removed the translational and rotational motion of the
protein w.r.t the C-alpha atom by the following command "trjconv -f
protein.xtc -o protein_fit.xtc -fit rot+trans". I choose C-alpha for the
least square fit. And finally g_dipoles command to calculate the dielectric
constant "g_dipoles -f protein_fit.xtc -o Mtot.xvg -eps epsilon.xvg -a
aver.xvg -d dipdist.xvg -c dipcorr.xvg". However, the dielectric constant
value (1.04) that I am getting is very less compared to the actual
dielectric constant (30).


Since the proteins have a net charge you have to translate them to their 
center of charge such that the leading term Q/r in Eqn 1 in the paper 
disappears (in the paper they use center of mass which is not strictly 
the same but a good approximation). The problem is that trjconv does not 
do this and therefore your net dipole moment is incorrect (since it is 
origin dependent). A roundabout way to fix this would be to compute the 
center of mass with g_traj (gmx traj) and multiply that by the total 
charge of the protein and subtract that from the dipole components. The 
compute epsilon yourself.



Dipole moment (Debye)
-
Average  = 172.7138  Std. Dev. =   7.4113  Error =   0.0524

The following averages for the complete trajectory have been calculated:

  Total < M_x > = 38.9789 Debye
  Total < M_y > = 54.2911 Debye
  Total < M_z > = -158.896 Debye

  Total < M_x^2 > = 1575.16 Debye^2
  Total < M_y^2 > = 3006.62 Debye^2
  Total < M_z^2 > = 25303.2 Debye^2

  Total < |M|^2 > = 29885 Debye^2
  Total |< M >|^2 = 29714.9 Debye^2

  < |M|^2 > - |< M >|^2 = 170.091 Debye^2

Finite system Kirkwood g factor G_k = 0.00570201
Infinite system Kirkwood g factor g_k = 0.00561463

Epsilon = 1.04819

Could you help me to find out what probably went wrong with the calculation?

Thanks,
Suman




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Lost particles while sorting

Re: [gmx-users] Lost particles while sorting

[gmx-users] Lost particles while sorting

[gmx-users] Problem using gmx wham

Re: [gmx-users] Problem on continuing MD

Re: [gmx-users] Problem on continuing MD

[gmx-users] Problem on continuing MD

Re: [gmx-users] Amino Acids

[gmx-users] Amino Acids

[gmx-users] Amino Acids

[gmx-users] Amino Acids

[gmx-users] Fwd: Amino acids

[gmx-users] force field for selinomethionine?

Re: [gmx-users] Problem in calculating static dielectric constant of Lysozymes

14 matches

Site Navigation

Mail list logo

Footer information